With the tremendous increase of neuroimaging data, there is a corresponding demand for usable, automated, and robust data analysis tools. Nipype is a mature Python library for efficient and flexible analysis of Big ?brain imaging? Data. Its reusable workflows can combine algorithms from a diverse set of existing software packages to generate reproducible results. The goal of this proposal is to further enhance the usability, functionality, and interoperability of Nipype and to widen its dissemination. This will increase its use by researchers and clinicians, boost its impact on biomedical research, and address many of its current limitations. Easier-to-use automation tools can reduce errors, lead to faster biomedical discoveries, and facilitate the transition from bench to bedside. From a software engineering standpoint, the goal is to offer a well-designed, cross-platform, and extensible dataflow computing solution that is intuitive and easy to use. We propose to build an interactive and intuitive web-based platform on top of the current extensive feature set of Nipype that interoperates with existing databases, software, and other workflow services. The result will be a generalizable, scalable, extensible, and tested infrastructure that minimizes complex programming interfaces to easier-to-use web applications. Nipype will still retain its extensible plugin architecture behind this web- based platform to allow continued inclusion of new software packages and algorithms, and execution on multiple platforms. Users will be able to use the most appropriate analysis strategies for their data. This platform will not only allow continued use of familiar software, but provide immediate exposure to the latest software tools for data analyses. For analysis, users will have access to complete provenance allowing others to reproduce their steps. We will interact with NeuroVault and NeuroSynth to provide a seamless transition between data, processing, sharing, and interpreting results. Finally, to sustain such an open and collaborative effort, we will train users and developers through hands-on workshops and webinars, encouraging them to take advantage of an expanding ecosystem for efficient and reproducible analysis. While the architecture will be initially deployed within the brain imaging community, we will adopt common standards to ensure interoperability with the greater biomedical imaging community. By continuing to engage the user community and extending the ecosystem for research computing, the project will lower the barrier for easy and efficient computation on large datasets, with the goal of faster development of treatment options.

Public Health Relevance

The proposed project aims to provide an open source, usable, efficient, robust, and scalable workflow software for biomedical data analysis. Providing open, free, and well-tested tools should enable users of brain imaging technologies to easily produce more detailed, consistent and reliable results. Efficient research coupled with greater access to large brain imaging data should lead to a better understanding of how the brain works and thereby directly impact approaches to diagnosing and treating neurological disorders.

National Institute of Health (NIH)
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Research Project (R01)
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Biodata Management and Analysis Study Section (BDMA)
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Weitz, Andrew Charles
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Massachusetts Institute of Technology
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United States
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Ghosh, Satrajit S; Poline, Jean-Baptiste; Keator, David B et al. (2017) A very simple, re-executable neuroimaging publication. F1000Res 6:124
Gorgolewski, Krzysztof J; Alfaro-Almagro, Fidel; Auer, Tibor et al. (2017) BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Comput Biol 13:e1005209
Klein, Arno; Ghosh, Satrajit S; Bao, Forrest S et al. (2017) Mindboggling morphometry of human brains. PLoS Comput Biol 13:e1005350
Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S et al. (2017) Diffeomorphic functional brain surface alignment: Functional demons. Neuroimage 156:456-465
Maumet, Camille; Auer, Tibor; Bowring, Alexander et al. (2016) Sharing brain mapping statistical results with the neuroimaging data model. Sci Data 3:160102
Margulies, Daniel S; Ghosh, Satrajit S; Goulas, Alexandros et al. (2016) Situating the default-mode network along a principal gradient of macroscale cortical organization. Proc Natl Acad Sci U S A 113:12574-12579